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{{Coexpression_clusters
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|full_id=C4029_Mast_tubular_mature_duodenum_brain_temporal_mesodermal
|id=C4029
|ontology_enrichment_celltype=CL:0000066!9.46e-09!254
|ontology_enrichment_disease=DOID:305!9.10e-09!106
|ontology_enrichment_uberon=UBERON:0001049!1.45e-20!57;UBERON:0005068!1.45e-20!57;UBERON:0006241!1.45e-20!57;UBERON:0007135!1.45e-20!57;UBERON:0005743!1.76e-20!86;UBERON:0007023!5.24e-20!115;UBERON:0001017!8.65e-20!82;UBERON:0000955!2.48e-19!69;UBERON:0006238!2.48e-19!69;UBERON:0002616!1.38e-18!59;UBERON:0000477!2.20e-17!286;UBERON:0003075!5.41e-17!86;UBERON:0007284!5.41e-17!86;UBERON:0000073!8.95e-17!94;UBERON:0001016!8.95e-17!94;UBERON:0004111!1.13e-16!241;UBERON:0003080!8.08e-16!42;UBERON:0002780!1.17e-15!41;UBERON:0001890!1.17e-15!41;UBERON:0006240!1.17e-15!41;UBERON:0000033!1.90e-15!123;UBERON:0002020!2.46e-15!34;UBERON:0003528!2.46e-15!34;UBERON:0002346!3.09e-15!90;UBERON:0001893!6.39e-15!34;UBERON:0001869!9.76e-15!32;UBERON:0000153!1.48e-14!129;UBERON:0007811!1.48e-14!129;UBERON:0000025!1.90e-14!194;UBERON:0002791!2.02e-14!33;UBERON:0002619!7.28e-14!22;UBERON:0000062!2.00e-13!511;UBERON:0000064!2.40e-13!219;UBERON:0001950!5.79e-13!20;UBERON:0003056!2.93e-12!61;UBERON:0000481!3.92e-11!347;UBERON:0000468!4.68e-11!659;UBERON:0000956!6.38e-11!25;UBERON:0000203!6.38e-11!25;UBERON:0000467!1.03e-10!625;UBERON:0000480!1.32e-10!626;UBERON:0004121!3.10e-10!169;UBERON:0000475!9.81e-10!365;UBERON:0000483!1.59e-09!309;UBERON:0000119!1.93e-09!312;UBERON:0000924!2.06e-09!173;UBERON:0006601!2.06e-09!173;UBERON:0000922!2.84e-09!612;UBERON:0002050!5.67e-09!605;UBERON:0005423!5.67e-09!605;UBERON:0000923!8.84e-09!604;UBERON:0005291!8.84e-09!604;UBERON:0006598!8.84e-09!604;UBERON:0002532!8.84e-09!604
}}

Latest revision as of 12:37, 17 September 2013


Full id: C4029_Mast_tubular_mature_duodenum_brain_temporal_mesodermal



Phase1 CAGE Peaks

Hg19::chr20:34680580..34680591,+p10@EPB41L1
Hg19::chr20:34680595..34680608,+p5@EPB41L1
Hg19::chr20:34680623..34680655,+p2@EPB41L1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell4.98e-08253
Uber Anatomy
Ontology termp-valuen
adult organism4.26e-20114
neural tube6.41e-2056
neural rod6.41e-2056
future spinal cord6.41e-2056
neural keel6.41e-2056
anatomical cluster7.38e-20373
central nervous system1.07e-1981
brain1.41e-1968
future brain1.41e-1968
regional part of nervous system6.87e-1953
regional part of brain6.87e-1953
organ system subdivision1.42e-17223
nervous system2.48e-1689
regional part of forebrain1.20e-1541
forebrain1.20e-1541
anterior neural tube1.20e-1541
future forebrain1.20e-1541
neural plate2.29e-1582
presumptive neural plate2.29e-1582
anatomical conduit3.21e-15240
brain grey matter3.50e-1534
gray matter3.50e-1534
telencephalon6.96e-1534
cerebral hemisphere9.14e-1532
regional part of cerebral cortex3.24e-1422
regional part of telencephalon4.23e-1432
neurectoderm1.27e-1386
neocortex1.73e-1320
tube3.58e-13192
organ part3.18e-12218
multi-tissue structure2.33e-11342
cerebral cortex4.68e-1125
pallium4.68e-1125
organ6.17e-11503
pre-chordal neural plate6.24e-1161
structure with developmental contribution from neural crest3.64e-10132
ectoderm-derived structure4.55e-10171
ectoderm4.55e-10171
presumptive ectoderm4.55e-10171
ecto-epithelium8.98e-10104
multi-cellular organism1.36e-09656
anatomical system1.90e-08624
embryo2.26e-08592
developing anatomical structure2.68e-08581
anatomical group3.04e-08625
epithelium7.88e-08306
cell layer9.30e-08309
embryonic structure4.68e-07564
germ layer7.14e-07560
germ layer / neural crest7.14e-07560
embryonic tissue7.14e-07560
presumptive structure7.14e-07560
germ layer / neural crest derived structure7.14e-07560
epiblast (generic)7.14e-07560
Disease
Ontology termp-valuen
carcinoma1.35e-08106


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.05336
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.15.56064
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.17.32221
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.348055
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.13.19905
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.8725
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0325832171342306
E2F6#187635.017155731697390.00791769806886330.0322762087671356
ELF1#199734.258097958807540.01295179875054610.0462942917180014
ZBTB7A#5134137.35190930787590.002516255860282270.0140397075431146



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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